How to make pictures in Bioblender
Looking at the PDB file of 1AD4 here, it looks like the PDB does not contain hydrogen. So you wouldn't see any Hydrogen atoms in the render. 

As for colouring different chains, you can import each chain by itself, and then use a surfacing algorithm (MLP or EP) to generate a surface, once you have the surface, it should be easy to apply the material yourself.

If you want to create something simple without fiddling with Blender as much, take a look at MolecularFlipbook.